Most of the sites I work with have asked to disable PM altogether and/or to choose e-mail as the only option (i.e. the default) for the site and to not archive member messages on the site. This gets rid of the need for pruning and managing this on the database as well as.
Further some sites wanted to allow members to choose whether or not to allow receipt of e-mail or not from other site users. We might also want to choose whether or not to allow anonymous vs. registered users to do so and/or by group permissions.
It's also possible that we could change PM into a module and remove it from the core. Then users can choose a best-in-class PM capability for their site that works for them.
Some of this I already have code for, some we would have to write.